A lot of my civilian ships are stuck with the orders to "Move to (planet) Trade Location" or "Load/Unload Colonists"
I've tried clearing their orders but they just go back to the same orders.
See below.
https://www. dropbox. com/s/w21vawkdr5agcf9/System_Map__16th_June_2083_2053_2015-10-12_13-47-17. png?dl=0
This doesn't sound like a bug. I think you are confusing the "Civilian" maintenance classification of the ships you design and build, with the Civilian ships that your actual civilian population designs and build. The latter can only be controlled in very limited ways by you (marking planets and systems out of bounds) and simply go from colony to colony, trading and moving colonists around.
That said, that naming convention comes from earlier versions of Aurora where your civilian populations couldn't design their own vessels, and simply used your "Civilian" blueprints that had reasonable components for their needs. Now that the Civilian populations do that themselves there is no connection between the "Civilian" ships that don't need maintenance and the actual civilian ships, so maybe the "doesn't need maintenance" classification should be renamed. Reliable, dependable, simple, something like that.